Ovarian follicular atresia is regulated by androgens directly via androgen receptors and indirectly after conversion to estrogens. The balance between proliferation and cell apoptosis is crucial for the physiological functioning of the follicles. The disorder between these processes leads to reproductive failure, such as cyst formation. Recent research suggests maternally or neonatally mediated effects of antiandrogen flutamide on reproductive functions during adulthood. Therefore, the current study was performed to determine whether late gestational or neonatal exposure to flutamide influences proliferation and apoptosis rates in large antral follicles of adult porcine ovary. These periods are critical in ovarian biology and may determine female fertility in adulthood. Flutamide was injected into pregnant gilts between days 80 and 88 of gestation, and into female piglets between days 2 and 10 postnatally. The ovaries were collected from treated and control adult pigs, and healthy large antral follicles were excised. In large antral follicles, granulosa and theca cells revealed elevated (p < 0.001) proliferation index measured by immunolocalization of Ki-67 following maternal and neonatal flutamide exposure. The percentage of apoptotic granulosa cells detected using TUNEL assay significantly decreased (p < 0.01) after flutamide administration, that paralleled with down-regulation (p < 0.01) of caspase-3 protein expression. Moreover, plasma testosterone decreased (p < 0.001) in flutamide-treated animals, whereas 17 beta-estradiol was elevated following flutamide exposure. The present research indicates increased proliferation and diminished apoptosis rates within large antral follicles of adult pigs following prenatal and neonatal flutamide administration, which might influence the normal development of the follicles and pigs fertility as a consequence.